An ID hypothesis: Front-loaded Evolution

Protein sequence comparisons allow us to look back over longer periods of time than DNA/mRNA sequences. Since we're talking about deep time here, I don't think it's even appropriate to do a BLAST search with an mRNA query.

For the record: I kinda buried my primary post with replies to individual comments, so my general response to objections to FLE can be found in my brief essay above.

Well, consider that:a. The E-values are not 1e-05. They are a bit less than that.b. An E-value of 1e-05 is not "bordering on noise" IMHO. Various investigators have used the E-value of 1e-04 as the cutoff value, yet their findings have been accepted by the scientific community.Of course, we have to look at the broader biological context here, too. In fact, I'm more than willing that the matches don't indicate front-loading. That's why I'm curious on this: do you think we'll ever find significant structural or sequence homologs of PAX6 in prokaryotes? I'm perfectly aware about the statistics of database matches. Edited by Genomicus, : No reason given.

Yes, but front-loading isn't about pre-programming something. It's about "stacking the deck," and anticipating the rise of plants and animals, for example. Simply put, if we start with an origin population of cells, which contain genes necessary for the development/function of plants and animals; next, this initial population separates into two populations. Then, deletion events in one population removes the animal genes, say, so that we just end up with plants. Alternatively, the front-loading designers could have designed such a population from the start: where some cells have genes for plants, and others have genes for animals.

Well, not when seen in the context of other biological features. In my little essay, I showed how (a) it is feasible for specific proteins to be front-loaded; (b) it is feasible for specific molecular machines to be front-loaded; and (c) how specific biochemical pathways can plausibly front-loaded. Thus, demanding that I explain the origin of the eye through FLE seems to be pushing the goal-posts back. The FLE hypothesis is just in its infancy; demanding that we produce a teleological hypothesis for the origin of the eye, at this point, seems a little premature, to me at least.

Yes.

See my response to Dr Adequate, above. True. Designing rhodopsin (or a homolog of rhodopsin) in the first genomes increases the likelihood that eyes will emerge precisely because the blind watchmaker doesn't have to tinker around with a totally unrelated protein, gradually transforming it into a protein that can be used for vision. If, however, rhodopsin (and other vision-related proteins) is designed into the first genomes, the fundamental ingredients for eye evolution are already in place, biasing evolution in favor of eye evolution. Few novel genes would have to evolve, and this significantly increases the chances of eye evolution.Rhodopsin would be available for co-option, but would it be the only possibility? Possibly the blind watchmaker would "generate" a protein that would then be co-opted into a vision-related function. But this would be an extra step: the blind watchmaker would have to duplicate an existing gene, modify it such that its function is compatible with a vision system, and then it'd be co-opted. These extra steps make it less likely for the eye to evolve in the absence of front-loading. From Wikipedia:
"Bacteriorhodopsin belongs to a family of bacterial proteins related to vertebrate rhodopsins, the pigments that sense light in the retina." (Emphasis added)Anyways, it was meant as an analogy - just to get the idea across.

How on earth would this be incompatible in any way with common ancestry? You'd simply design cell population A with genes that would be later used by plants, and cell population B with genes that would be later used by animals. These two populations, on the whole, would be genetically related, with the exception of the different plant/animal genes. Not meaning to dodge this question, but I think Mr Jack has answered this question succinctly. I really don't see how I seem to be abandoning common ancestry.

Not at all. Perhaps I'm not being clear here. I'm simply saying that the first life forms that were seeded on earth could contain different sets of genes, one for plants, and one for animals. Evolution would follow from there, shaped around the initial constraints. There is no constant intervention/tinkering from any intelligence.

Remember, the purpose of this discussion - at least my purpose of this discussion - and that is for the FLE hypothesis to be refined. Before submitting any FLE hypothesis to the scientific community, it's not a bad idea to see what the bio guys and gals over here at EvC think about the FLE hypothesis, dontcha think? This helps in pointing out the weak spots and strong spots in the hypothesis, and indicates which parts need to be developed more rigorously.

Yes, and based on phylogenetic considerations, I don't think my idea of two different initial populations is tenable.

Chance. What's stopping animal genes in one lineage from being deleted? What's stopping a plant lineage to start developing, built around plant genes, and thus animal genes would be eliminated in this lineage (or become pseudogenes)?

Chance has always been a factor in the FLE hypothesis. Biology is a probabilistic science - the outcome was not inevitable, but certainly the odds were considerably in its favor.Consider the following example: the last common ancestor of plants and animals have genes x (an animal gene) and y (a plant gene). In one of these lineages, a series of mutations occur, generating a new morphological structure such that gene x is necessary for the existence of the new lineage. Gene y is dispensable, and so it is lost in this lineage. An analogous process occurs in a second lineage, albeit in reverse: instead of gene y being lost, gene x is lost.

If by "the dice were loaded" you mean the outcome was inevitable, then no. But under the FLE hypothesis, the outcome that resulted was far more probable than in the absence of front-loading. The first genomes anticipated the origin of plants and animals, for example.

Actually, I thought that was sufficiently clear: that the blind watchmaker tinkers with the initial constraints, and it shapes its designs around those initial constraints. Multi-cellular life forms, plants and animals, possibly invertebrates and vertebrates; specific taxonomic classes could be anticipated by the first genomes, but they weren't necessarily front-loaded. Still, any "anticipation" would make the appearance of a specific biological feature much more probable. One reason chance is a factor is because you can't stop the blind watchmaker - but you can put it to work for you if you start with right initial constraints. Edited by Genomicus, : No reason given.